Master Class on HPC Applications
For Life Sciences
A CloudAsia2010 Satellite Workshop

  


Job Submission

Documentation

Workshop

Introduction

Registration

Programme

Workshop Faculty
and Speakers

Workshop Materials

AMBIS Annual
Lecture

Venue Map

Accommodation

Contact Us
Printable version

(NEW!) Training materials for the workshop are available here

HIGHLIGHTS

  1. CloudAsia 2010 Opening Ceremony
    Date: 4th May 2010, 8.30am-10.30am
    Venue: Singapore Management University, Main Auditorium
    1. Opening Address (9:00am - 9:10am)
      RADM (NS) Ronnie Tay, Chief Executive, Infocomm Development Authority of Singapore
    2. Keynote Address (9.10am - 10.00am)
      "Extending the Cloud Value Chain: Lessons Learned and Beyond"
      Alan Ganek(CTO & VP of Strategy & Technology, Software Group, IBM)

    All EUAsiaGrid participants are invited to attend
    Bus provided to transfer participants from CloudAsia 2010 to NUS for late morning start of workshop at computer lab

  2. EUAsiaGrid Workshop Keynotes
    Date: 4th May 2010, 11.30pm to 2.15pm
    Venue: Block S13, CSD Computer Labs (Level 4),
    Department of Physics, National University of Singapore
    1. "EUAsiaGrid: a standard computational platform for eScience"
      Professor Ludek Matyska, CESNet and Masaryk University, Czech Republic
    2. "Core Technology of World Wide Grid and gLITE MiddleWare"
      Professsor Marco Fargetta, Training Director, EUAsiaGrid and Senior Researcher, INFN, Italy

  3. AMBIS Annual General Meeting and Dinner and Annual Lecture
    Date: 5th May 2010, 7pm to 9.30pm
    Venue: Function Room, The Scholar Restaurant, NUS Guild House
    Kent Ridge Guild House
    Annual AMBIS Lecture:

    "Towards a Global Computational Infrastructure for eScience"
    Professor Simon Lin, Director,
    Supercomputing Center, Academia Sinica, Taiwan.

PROGRAMME SCHEDULE

Tuesday 4 May 2010
8.30am-10.30am CloudAsia 2010 Opening Ceremony at Singapore Management University
10.30am-11.30am Arrive at NUS workshop venue, Dept of Physics
Opening Session
Session Chair: Dr Asif Khan
11.30am-12pm Keynote Speaker:
Professor Ludek Matyska: EUAsiaGrid: a standard computational platform for eScience
Powerpoint Presentation
12pm-12.30pm Biomedical Applications of Grid Computing
Powerpoint Presentation
12.30pm-1.30pm Lunch
Workshop Session I
1.30pm-2.15pm Keynote Speaker:
Professor Marco Fargetta: Core Technology of World Wide Grid and gLITE MiddleWare
 Link to presentation ppt
2.15pm-4pm Discussion and Hands-on session
Session Chairs: Professors Marco Fargetta & Giuseppe La Rocca
All training materials here
4pm-4.30pm Tea Break
Workshop Session II: Discussion and Hands-on session
Session Chairs: Professors Marco Fargetta & Giuseppe La Rocca
4.30pm-6.30pm Core concepts and technology on gLite middleware - security, job management, data management and grid information system
http://www.euasiagrid.org/wiki/index.php/Training_materials_and_other_resources
 
Wednesday 5 May 2010
Workshop Session III: Application Porting and Grid Integration
Session Chairs: Professors Simon Lin & Tan Tin Wee
9.30am-10.30am 1. Grid enabling phylogenetic inference
   a) of HIV sequences (Hu Yongli, NUS) HIV.ppt
   b) of dengue and other flavivirus sequences
       (Chanditha Hapuarachchi, NEA Singapore)
      NEA.ppt
10.30am-11am 2. Grid enabling parameter sweep for SVM parameter optimization of caspase cleavage sites prediction (Lawrence Wee, I2R, Singapore)
SVM.ppt
11.00am-12.30pm 4. Grid enabling genome search
    a) to identify T3SS effectors
      (Sun Guang Wen, NUS) T3Effectors.ppt
12.30pm-1.30pm Lunch
Workshop Session IV: Application Porting and Grid Integration
Session Chairs: Professors Simon Lin & Tan Tin Wee
1.30pm-2pm 5. Grid Enabling AutoDock Ligand-Receptor Docking
   a. for HLA-ligand complexes (Lam Tze Hau)                 autodock.ppt
   b. and Gromacs (Heru Suhartanto, Univ of
      Indonesia) gromacs.ppt
2pm-4pm Discussion Session
4pm-4.30pm Tea Break
Workshop Session V: Discussion Session
Session Chairs: Professors Simon Lin & Tan Tin Wee
4.30pm-6.30pm Examples from EUAsiaGrid:
Drug discovery/GVSS Virtual Screening on Avian Flu and Dengue Fever, WISDOM (Wide In Silico Docking on Malaria)
1. Grid Application Platform, TWGrid: http://gap.grid.sinica.edu.tw/
6.30pm-7pm Arrive at Kent Ridge Guild House (by internal shuttle bus)
7pm-9.30pm AMBIS AGM/Dinner and Annual Lecture
Professor Simon Lin: Towards a Global Computational Infrastructure for eScience
Presentation PPT Huge 10Mbytes!
 
Thursday 6 May 2010
Workshop Session VI: Sharing and Discussion Session
9am-11.30am Application porting technology, tools, and methodologies to gLite
11.30am-12.30pm Invited Speaker:
Simone Brunozzi: Grids or clouds?
Presentation PPT
12.30pm-1.30pm Lunch
Workshop Session VII
1.30pm-2.45pm Practical Parallel Computing in R
Xie Chao and Tan Tin Wee, National University of Singapore
Tutorial Notes on parallelR
Tutorial Slides on parallelR
Brief Introduction to R for Beginners
Workshop Session VIII
2.45pm-4pm Cloud Computing with BioSlax and NUS BioCloud
Mark De Silva, Lim Kuan Siong and Tan Tin Wee, National University of Singapore
Tutorial materials
4pm-4.30pm Tea Break
4.30pm-5pm Demonstration and Reports on Application Porting
5pm Closing Ceremony

 First Created: 25, 28 March 2010, Last Updated: 6 May 2010